MolNFT v1 · #176709 · protein
A complex of a new GH20 enzyme from bacteroides thetaiotaomicron
7DVA · Beta-N-acetylhexosaminidase: “A complex of a new GH20 enzyme from bacteroides thetaiotaomicron”. X-ray diffraction, 1 ligand (NGS), 6 pockets (best druggability 0.82). MolNFT v1 #176709 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DVA
- Type
- protein
- Length
- 1,045 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-N-acetylhexosaminidase
- EC
- 3.2.1.52
- UniProt
- A0A0P0FIE8
- Ligands
- NGS
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 522 | 37% helix, 19% strand | A0A0P0FIE8 |
| A | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 523 | 36% helix, 20% strand | A0A0P0FIE8 |
Ligands and binding sites
- NGS · 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose · ligand · 2 copies · chains B, A
- GOL · Glycerol · additive · 5 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.82 | 0.83 | 91 | GOL, NGS |
| 2 | 277 | 0.77 | 0.89 | 38 | empty |
| 3 | 134 | 0.52 | 0.80 | 19 | NGS, GOL |
| 4 | 121 | 0.48 | 0.79 | 25 | empty |
| 5 | 94 | 0.32 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- B–A · 1020 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7DVA · Structure of wild type Bt4394, a GH20 family sulfoglycosidase, in complex with 6S-GlcNAc · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A0P0FIE8
- Elsewhere: RCSB PDB 7DVA · PDBe 7DVA · UniProt A0A0P0FIE8
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